I agree that Notability and Goodnotes work very well with Pencil....
For the pencil, neither is great. I would use a different app for pencil note taking.
I would keep typed notes and and files seperate to handwritten notes, or choose which input method you use more.
If you mainly use the pencil, go with notability/goodnotes. If you mainly type, go with onenote/Evernote. Whichever suits your style best.